This paper presents a supervisory multi-agent control policy over an acoustic communication network subject to imperfections (packet dropout and transmission delay) for localisation of an underwater flow source (e.g., source of chemical pollution, fresh water, etc.) with an unknown location at the bottom of the ocean. A two-loop control policy combined with a coding strategy for reliable communication is presented to perform the above task. A simulator is developed and used to evaluate the trade-offs between quality of communication, transmission delay and control for a fleet of autonomous underwater vehicles supervised over a noisy acoustic communication network by an autonomous surface vessel. It is illustrated that without compensation of the effects of severe random packet dropout, localisation of an unknown underwater flow source is not possible for the condition simulated just by implementing a two-loop control policy. But a two-loop control policy combined with a strategy for reliable communication locates the unknown location of flow source.